Orthologs

Supporting materials for PLoS ONE 2014 article:

Ward N, Moreno-Hagelsieb G (2014) Quickly Finding Orthologs as Reciprocal Best Hits with BLAT, LAST, and UBLAST: How Much Do We Miss? PLoS ONE 9, e101850.

Please find tables with homologs as found by each program tested and corresponding RBHs following this link.

The format for results is the same we would obtain from the “-outfmt 6” option under BLAST+, or the “-m 8” option under legacy BLAST. RBHs add a last column indicating that a putative ortholog is either a RBH, or a fusion. Tables with counts can be found here.

Supporting material for 2008 article:

NOTE: NCBI has released a completely re-programed BLAST suite called BLAST+. We found that the options we tested in our 2008 article with legacy BLAST work similarly with BLAST+. If you wish to further test these options using BLAST+ consult the table below:

Equivalent options for Masking and alignment types between legacy BLASTP and BLASTP+ (some options cannot be stated explicitly in BLAST+)